Merge pull request #41 from Isabelle-inrae/patch-5-phis-lightened

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manuscript.html

@@ -92,8 +92,8 @@
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@@ -236,9 +236,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/21f6e85351f788a6c8622f144263e605296f4751/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f8e55569f5cb11fe0ecc7954df3385314242aa77">plantbreeding/BrAPI-Manuscript2@f8e5556</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/21f6e85351f788a6c8622f144263e605296f4751">plantbreeding/BrAPI-Manuscript2@21f6e85</a>
 on May 7, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -646,16 +646,10 @@ <h3 id="data-management">Data Management</h3>
 * Alternate solutions/ why is it better with BrAPI
 * future related use cases, areas to improve -->
 <h4 id="phis">PHIS</h4>
-<p>The Hybrid Phenotyping Information System (<a href="http://www.phis.inrae.fr/">PHIS</a><span class="citation" data-cites="OodVqG7n">[<a href="#ref-OodVqG7n" role="doc-biblioref">3</a>]</span>), based on the <a href="https://github.com/OpenSILEX/">OpenSILEX</a> framework, assumes responsibility for the systematic collection and management of data from phenotyping and high-throughput phenotyping experiments on a day-to-day basis. PHIS has the ability to efficiently store, organize and manage a wide range of data sets, including images, spectra and growth curves. This functionality extends to data at multiple spatial and temporal scales, from leaf to canopy, from a variety of sources such as field and greenhouse environments.</p>
-<p>A key feature of PHIS is the unambiguous identification of all objects and traits within an experiment, establishing consistent relationships between them through the application of ontologies and semantics. This approach is designed to adapt to variations in experimental conditions, whether in the field or in controlled environments. PHIS’s ontology-driven architecture emerges as a robust tool for integrating and managing data derived from diverse experiments and platforms, facilitating the creation of meaningful relationships between objects and augmenting datasets with relevant knowledge and metadata.</p>
-<p>Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment (<a href="https://www.miappe.org/">MIAPPE</a><span class="citation" data-cites="TVXmHLRk">[<a href="#ref-TVXmHLRk" role="doc-biblioref">4</a>]</span>) and the Breeding API (BrAPI) standards.</p>
-<p>The system recommends specific naming conventions, fostering a standardized approach for users to declare their resources. Notably, PHIS is widely adopted by various experimental platforms of the national <a href="https://www.phenome-emphasis.fr/">PHENOME</a> and European <a href="https://emphasis.plant-phenotyping.eu/">EMPHASIS</a> infrastructure, serving as a hub for data management.
-Moreover, dedicated instances of PHIS have been established for the explicit purpose of resource sharing, encompassing projects, genetic resources, and variables, thereby fostering collaborative engagement and the dissemination of knowledge pertaining to studied concepts.</p>
-<h5 id="phis-brapi">PHIS &amp; BrAPI</h5>
-<p>PHIS offers a RESTful API designed to streamline interaction with data within a platform. Within this API, various services aligning with the Breeding API (BrAPI) standards have been implemented, encompassing the Core, Phenotyping, and Germplasm modules. Comprehensive documentation for these services is available on the PHIS Swagger interface. This integration with Swagger ensures that users can easily access, understand, and utilize the functionalities provided by the BrAPI-compliant web services, fostering transparency and facilitating effective engagement with the PHIS platform.</p>
-<p>The design and development of PHIS have been meticulously tailored, incorporating the explicit constraint of aligning with BrAPI requirements. This intentional alignment ensures that PHIS adheres to the specified standards and protocols outlined by the Breeding API (BrAPI), thereby fostering seamless integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as a substantial foundation for formalizing the data model, simultaneously facilitating compatibility with other standards, such as MIAPPE. Thus, by consciously incorporating BrAPI requirements into its structure, PHIS not only meets the phenotyping domain standards but also enhances its capacity for interoperability and effective collaboration within the broader context of plant breeding and related domains.</p>
+<p>The Hybrid Phenotyping Information System (<a href="http://www.phis.inrae.fr/">PHIS</a><span class="citation" data-cites="OodVqG7n">[<a href="#ref-OodVqG7n" role="doc-biblioref">3</a>]</span>), based on the <a href="https://github.com/OpenSILEX/">OpenSILEX</a> framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the national <a href="https://www.phenome-emphasis.fr/">PHENOME</a> and European <a href="https://emphasis.plant-phenotyping.eu/">EMPHASIS</a> infrastructure. It manages and collects data from Phenotyping and High Throughput Phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.</p>
+<p>PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment (<a href="https://www.miappe.org/">MIAPPE</a><span class="citation" data-cites="TVXmHLRk">[<a href="#ref-TVXmHLRk" role="doc-biblioref">4</a>]</span>). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields.</p>
 <p>The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in <a href="https://urgi.versailles.inra.fr/faidare/">FAIDARE</a> very easy to implement.</p>
-<p>Indeed, as PHIS offers BrAPI-compliant Web Services, this greatly simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating seamless communication and collaboration between PHIS and other systems within the European context. This interoperability not only streamlines data sharing but also promotes a more cohesive and effective approach to managing and utilizing phenotyping data across diverse platforms and research initiatives in the European scientific community.</p>
+<p>Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.</p>
 <h4 id="deltabreed">DeltaBreed</h4>
 <!-- Shawn Y.-->
 <p>DeltaBreed is an open-source data management system designed and developed by Breeding Insight to support USDA-ARS specialty crop and animal breeders. DeltaBreed is a unified system for managing breeding data that connects a variety of BrAPI applications (see list below). BrAPI integration allows the complexity underlying interoperability to be hidden, shielding users from multifactorial differences between diverse applications. DeltaBreed, adhering to the BrAPI model, establishes data standards and validations for users and provides a singular framework for data management and user training.</p>

manuscript.md

@@ -63,8 +63,8 @@ header-includes: |
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   <meta name="citation_publication_date" content="2024-05-07" />
   <meta property="article:published_time" content="2024-05-07" />
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-  <meta property="article:modified_time" content="2024-05-07T18:01:38+00:00" />
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@@ -212,9 +212,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/21f6e85351f788a6c8622f144263e605296f4751/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@f8e5556](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f8e55569f5cb11fe0ecc7954df3385314242aa77)
+from [plantbreeding/BrAPI-Manuscript2@21f6e85](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/21f6e85351f788a6c8622f144263e605296f4751)
 on May 7, 2024.
 </em></small>
 
@@ -704,24 +704,13 @@ BrAPI has further increased the value of GridScore by integrating it into the ov
 
 #### PHIS 
 
-The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/)[@doi:https://doi.org/10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) framework, assumes responsibility for the systematic collection and management of data from phenotyping and high-throughput phenotyping experiments on a day-to-day basis. PHIS has the ability to efficiently store, organize and manage a wide range of data sets, including images, spectra and growth curves. This functionality extends to data at multiple spatial and temporal scales, from leaf to canopy, from a variety of sources such as field and greenhouse environments.
+The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/)[@doi:https://doi.org/10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the national [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) infrastructure. It manages and collects data from Phenotyping and High Throughput Phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.
 
-A key feature of PHIS is the unambiguous identification of all objects and traits within an experiment, establishing consistent relationships between them through the application of ontologies and semantics. This approach is designed to adapt to variations in experimental conditions, whether in the field or in controlled environments. PHIS's ontology-driven architecture emerges as a robust tool for integrating and managing data derived from diverse experiments and platforms, facilitating the creation of meaningful relationships between objects and augmenting datasets with relevant knowledge and metadata.
-
-Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/)[@doi:https://doi.org/10.1111/nph.16544]) and the Breeding API (BrAPI) standards. 
-
-The system recommends specific naming conventions, fostering a standardized approach for users to declare their resources. Notably, PHIS is widely adopted by various experimental platforms of the national [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) infrastructure, serving as a hub for data management. 
-Moreover, dedicated instances of PHIS have been established for the explicit purpose of resource sharing, encompassing projects, genetic resources, and variables, thereby fostering collaborative engagement and the dissemination of knowledge pertaining to studied concepts.
-
-##### PHIS & BrAPI
-
-PHIS offers a RESTful API designed to streamline interaction with data within a platform. Within this API, various services aligning with the Breeding API (BrAPI) standards have been implemented, encompassing the Core, Phenotyping, and Germplasm modules. Comprehensive documentation for these services is available on the PHIS Swagger interface. This integration with Swagger ensures that users can easily access, understand, and utilize the functionalities provided by the BrAPI-compliant web services, fostering transparency and facilitating effective engagement with the PHIS platform.
-
-The design and development of PHIS have been meticulously tailored, incorporating the explicit constraint of aligning with BrAPI requirements. This intentional alignment ensures that PHIS adheres to the specified standards and protocols outlined by the Breeding API (BrAPI), thereby fostering seamless integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as a substantial foundation for formalizing the data model, simultaneously facilitating compatibility with other standards, such as MIAPPE. Thus, by consciously incorporating BrAPI requirements into its structure, PHIS not only meets the phenotyping domain standards but also enhances its capacity for interoperability and effective collaboration within the broader context of plant breeding and related domains.
+PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/)[@doi:https://doi.org/10.1111/nph.16544]). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields.
 
 The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in [FAIDARE](https://urgi.versailles.inra.fr/faidare/) very easy to implement.
 
-Indeed, as PHIS offers BrAPI-compliant Web Services, this greatly simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating seamless communication and collaboration between PHIS and other systems within the European context. This interoperability not only streamlines data sharing but also promotes a more cohesive and effective approach to managing and utilizing phenotyping data across diverse platforms and research initiatives in the European scientific community.
+Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.
 
 #### DeltaBreed